Web Service Dedicated to Metabolism

Training Meeting
Microme

–

Marseilles

-

28/03/2012.

David
Vallenet
, François
Le
Fèvre
, Damien
Mornico
,

Maria Jose Lopez, Eugenio
Belda
,
Claudine
Médigue

Web Service

Dedicated
to Metabolism

Laboratory of Bioinformatic Analysis in Genomic and Metabolism (LABGeM team)

CEA/DSV/IG/Genoscope & CNRS UMR8030

Some of
the
Microme

‘s needs

Data Retrieval

•
Specific

•
Dump of data

Services

•
exposition of expert methods
(read access)

•
integration of expert methods
(write access)

WEB SERVICE

3/30/2012

CEA / LABGeM partner
-

Microme Training

2

CEA Accessible Data / Information

Compound :
Chebi

Reaction : Rhea

GPR : MicroScope

Pathway: Microscope

Genomic : Microscope

Phenotype: Microscope

PREDICTED

& EXPERT
CURATION

3/30/2012

CEA / LABGeM partner
-

Microme Training

3

Web service to retrieve the Gene Protein Relationship


3/30/2012

CEA / LABGeM partner
-

Microme Training

4

Metabolic workflow

Data retrieval layer

Application design

Model insight

Available services

Analyzing results

Metabolic Workflow

pkgdb

MicroCyc

PGDB

MicroDb

PathoLogic

Formatter

Complexes

Generator

MicroDB

Generator

Expert validation

Automatic pipeline

3/30/2012

CEA / LABGeM partner
-

Microme Training

5

Data Retrieval Layer

MicroDb

Web Service

MicroScope

MicroCyc Web

PkGDB

MicroScope

3/30/2012

CEA / LABGeM partner
-

Microme Training

6

Application Design


UML specification


Automatic generation


Back end


Persistence


Entity


Services


Technologies


Java (Hibernate/Spring)


Maven


AndroMDA


http://www.andromda.org/docs/index.html

3/30/2012

CEA / LABGeM partner
-

Microme Training

7

From PGDB to reaction

3/30/2012

CEA / LABGeM partner
-

Microme Training

8

Gene Protein Relationship

3/30/2012

CEA / LABGeM partner
-

Microme Training

9

Protein Reaction Relationship

3/30/2012

CEA / LABGeM partner
-

Microme Training

10

Available Service 1.0

3/30/2012

CEA / LABGeM partner
-

Microme Training

11

Accessible Genomes

Hamap

code

Microscope id

BioCyc

version

3/30/2012

CEA / LABGeM partner
-

Microme Training

12

Gene Details



Id MicroScope

Id MicroCyc

Id
UniProt

Id
RefSeq

Evidence Genomic

•
Automatic: Transfert of annotation

•
Validated: Human Expert Curation

3/30/2012

CEA / LABGeM partner
-

Microme Training

13

Complex Encoding

<
ns:gprSimpleVO

xsi:type
="
ns:GprSimpleVO
">


<
ns:associatedGenes
>


<
ns:geneSimpleVO

xsi:type
="
ns:GeneSimpleVO
">


<ns:accession1>GO145023</ns:accession1>



<
ns:frame
>G2NI
-
1492</
ns:frame
>


<
ns:id
>14363</
ns:id
>


<
ns:shortName
>
linC
</
ns:shortName
>


</
ns:geneSimpleVO
>


<
ns:geneSimpleVO

xsi:type
="
ns:GeneSimpleVO
">


<
ns:accession1>GO145024</
ns:accession1>


<
ns:frame
>G2NI
-
1493</
ns:frame
>


<
ns:id
>14364</
ns:id
>


<
ns:shortName
>
linD
</
ns:shortName
>


</
ns:geneSimpleVO
>

</
ns:associatedGenes
>


<
ns:catalyzedReactionCommonName
>ACIAD1575_linCD</
ns:catalyzedReact
ionCommonName
>

<
ns:ecNumber
>1.14.99.28</
ns:ecNumber
>

<
ns:frameReaction
>LINALOOL
-
8
-
MONOOXYGENASE
-
RXN</
ns:frameReaction
>

<
ns:gpr
>G2NI
-
1492</
ns:gpr
>

<
ns:gprEvidence
>
validated
</
ns:gprEvidence
>

<
ns:reactionCommonName
>
linalool

8
-
monooxygenase</
ns:reactionCommonName
>

</
ns:gprSimpleVO
>

GO145023

GO145024

RXN0
-
2606

Id MicroCyc

G(P)R

Evidence

3/30/2012

CEA / LABGeM partner
-

Microme Training

14

Isozyme

Encoding or putative Complex?

<
ns:gprSimpleVO

xsi:type
="
ns:GprSimpleVO
">


<
ns:ecNumber
>NIL</
ns:ecNumber
>


<
ns:frameReaction
>DISULFOXRED
-
RXN</
ns:frameReaction
>


<
ns:gpr
>GEL
-
4936@EB7Av1_1080005_dsbA$GO3290285</
ns:gpr
>


<
ns:gprEvidence
>
predicted
</
ns:gprEvid
ence
>

</
ns:gprSimpleVO
>


<
ns:gprSimpleVO

xsi:type
="
ns:GprSimpleVO
">


<
ns:ecNumber
>NIL</
ns:ecNumber
>


<
ns:frameReaction
>DISULFOXRED
-
RXN</
ns:frameReaction
>


<
ns:gpr
>GEL
-
1163@EB7Av1_90089_dsbC$GO3286552</
ns:gpr
>


<
ns:gprEvidence
>
predicted
</
ns:gprEvid
ence
>

</
ns:gprSimpleVO
>


<
ns:gprSimpleVO

xsi:type
="
ns:GprSimpleVO
">


<
ns:ecNumber
>NIL</
ns:ecNumber
>


<
ns:frameReaction
>DISULFOXRED
-
RXN</
ns:frameReaction
>


<
ns:gpr
>GEL
-
2576@EB7Av1_290029_dsbG$GO3287959</
ns:gpr
>


<
ns:gprEvidence
>
predicted
</
ns:gprEvid
ence
>

</
ns:gprSimpleVO
>


GO3290285

GO3286552

GO3286297

DISULFOXRED
-
RXN

GO3290285

GO3286552

GO3286297

DISULFOXRED
-
RXN

3/30/2012

CEA / LABGeM partner
-

Microme Training

15

Storing and managing growth phenotype

3/30/2012

CEA / LABGeM partner
-

Microme Training

16

Growth phenotype

Model proposition

Growth phenotype

Objective

•
Store the result of growth phenotype experiment

•
Query methods

•
Relationship with genomic annotation

•
Relationship with models

Difficulties

•
What is a growth phenotype results (0
-
1 ?)

•
How to manage replicates ?

•
How to integrate expert curation ?

•
How to interpolate result ? (0
-
1


auxotrophy)

3/30/2012

CEA / LABGeM partner
-

Microme Training

17

Experiment


3/30/2012

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-

Microme Training

18

Growth Phenotype

3/30/2012

CEA / LABGeM partner
-

Microme Training

19

Medium

3/30/2012

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-

Microme Training

20

Strain

3/30/2012

CEA / LABGeM partner
-

Microme Training

21

3/30/2012

CEA / LABGeM partner
-

Microme Training

22

Other projects

Outlook

Training

Other projects in development

3/30/2012

CEA / LABGeM partner
-

Microme Training

23

Main Entry point

http://www.genoscope.cns.fr/microme/

3/30/2012

CEA / LABGeM partner
-

Microme Training

24

Interactions Outlook &






Open Questions

W
e
b

S
e
r
v
i
c
e

MicroScope

WebService

/ UI / Web

GPRs

Microme

Update
Frequency?

Integration

Process ?

Partner
Tools

CEATools

Integration

Process ?

3/30/2012

CEA / LABGeM partner
-

Microme Training

25

Training with
webservice

Generation
of java
client

Query
several
webservices

Manipulate
the data

3/30/2012

CEA / LABGeM partner
-

Microme Training

26

Thanks for Interaction


ULB partner


Jacques van
Helden


Didier
Croes


Quentin
Dacosta


Jonathan
Verneau


CERTH partner


Christos
Ouzounis


Fotis

Psomopoulos

3/30/2012

CEA / LABGeM partner
-

Microme Training

27